Grab the Switch master keys and save them as keys.dat in the same folder as hactool: <link removed - just Google for "Nintendo Switch master keys"

Extract the game NSP (it's just a container) with hactool:

hactool -t pfs0 -k keys.dat <nameofthegamensp.nsp> --outdir=mk11

it will output a few NCAs files, you only care about the big one (about 7 gigs) which is the game image. Keep that, you'll need it. Let's refer to this NCA as "base NCA".

From there you can choose to extract it, and ignore the update, but you can also extract the updated game (basically merging both, switch updates are not extra files, they are "patch files", patching the 1.00 filesystem).

To extract the updated game:

Extract the day1 patch NSP using the same command as before.

Same as before, keep the biggest NCA (around 17 gigs). I'll refer this as the "patch NCA"